There has been plenty of discussion here about how footnotes work in kepubs. The official word is in
https://github.com/kobolabs/epub-spe...kobo-platforms. And that is basically that the links and anchors have to be setup correctly. And, unless the book is using the epub3 syntax for the footnotes, the software is taking a guess as to whether the link is a footnote or not. From the experience here, it doesn't always work exactly as described, so there is probably more that hasn't been documented there.